Contacts of the helix formed by residues 59 - 70 (chain C) in PDB entry 1SZU
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with HIS 59 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55C THR* 3.4 32.1 - - - +
56C GLY 3.8 2.0 + - - -
57C HIS 3.3 4.4 + - - -
58C LEU* 1.3 71.9 - - - +
60C PRO* 1.3 80.5 - - + +
61C LYS* 3.2 35.0 + - + +
62C VAL* 3.0 24.5 + - + +
63C VAL* 2.9 21.9 + - - +
272C GLY 5.8 0.4 + - - -
314C VAL* 3.5 16.6 - - + +
318C GLU* 2.8 38.1 + - - -
404C THR* 4.3 7.2 - - + -
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Residues in contact with PRO 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C LEU 3.1 8.0 - - - +
59C HIS* 1.3 96.2 - - + +
61C LYS* 1.3 60.0 + - + +
63C VAL* 3.7 7.0 - - + +
64C ALA* 3.0 28.9 + - - +
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Residues in contact with LYS 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C HIS* 3.2 25.1 + - + +
60C PRO* 1.3 79.2 - - + +
62C VAL* 1.3 63.4 + - - +
64C ALA* 3.3 8.3 + - + +
65C ALA* 3.1 17.5 + - - +
310C GLU* 3.3 28.2 - - - +
314C VAL* 3.9 11.9 - - + -
317C GLN* 4.7 15.3 - - - +
318C GLU* 4.7 2.7 - - - +
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Residues in contact with VAL 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C THR* 4.7 3.4 - - - +
58C LEU* 6.2 0.4 - - - -
59C HIS* 3.0 28.8 + - + +
61C LYS* 1.3 77.2 - - - +
63C VAL* 1.3 58.7 + - + +
65C ALA* 3.1 4.0 + - - +
66C VAL* 2.9 28.1 + - - +
271C ALA 4.7 1.1 - - - +
272C GLY 5.0 3.4 - - - +
274C PHE* 3.9 27.4 - - + -
307C ALA* 4.0 17.9 - - + +
310C GLU* 3.7 10.5 - - + -
311C VAL* 3.7 39.5 - - + +
314C VAL* 4.7 3.1 - - + -
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Residues in contact with VAL 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C LEU* 3.7 40.6 - - + +
59C HIS 2.9 21.7 + - - +
60C PRO* 3.7 7.0 - - + +
62C VAL* 1.3 76.8 - - + +
64C ALA* 1.3 59.0 + - - +
66C VAL* 3.2 8.0 + - - +
67C GLU* 2.8 56.9 + - + +
274C PHE* 5.6 2.0 - - + -
70D LEU* 4.4 18.6 - - + +
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Residues in contact with ALA 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C PRO 3.0 18.2 + - - +
61C LYS* 3.6 8.5 - - + +
62C VAL 3.3 0.2 - - - -
63C VAL* 1.3 78.7 - - - +
65C ALA* 1.3 61.2 + - - +
67C GLU* 3.3 12.4 + - - +
68C ALA* 3.0 23.9 + - - +
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Residues in contact with ALA 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C LYS 3.1 12.5 + - - +
62C VAL 3.1 8.0 + - - +
64C ALA* 1.3 74.4 - - - +
66C VAL* 1.3 65.8 + - - +
68C ALA* 3.2 7.2 + - - +
69C GLN* 3.0 18.7 + - - +
306C VAL* 3.7 35.5 - - + +
310C GLU* 3.9 17.9 - - + +
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Residues in contact with VAL 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C VAL 2.9 17.6 + - - +
63C VAL* 3.5 9.4 - - - +
65C ALA* 1.3 76.1 - - - +
67C GLU* 1.3 57.9 + - - +
69C GLN* 3.2 3.8 + - - +
70C LEU* 2.9 31.3 + - + +
274C PHE* 3.7 28.7 - - + -
303C ILE* 3.5 27.2 - - + +
306C VAL* 4.1 6.7 - - - +
307C ALA* 4.0 20.4 - - + -
66D VAL* 6.3 1.3 - - + -
70D LEU* 3.7 27.6 - - + -
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Residues in contact with GLU 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C VAL* 2.8 46.2 + - + +
64C ALA* 3.7 10.6 - - - +
66C VAL* 1.3 74.1 - - - +
68C ALA* 1.3 62.6 + - - +
70C LEU* 3.3 21.8 + - + +
71C LYS* 3.5 20.7 + - - +
67D GLU* 5.3 8.3 - - + +
70D LEU* 3.8 22.9 - - + +
71D LYS* 5.5 8.8 - - - +
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Residues in contact with ALA 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C ALA 3.0 16.7 + - - +
65C ALA* 3.2 6.7 + - - +
67C GLU* 1.3 76.2 - - - +
69C GLN* 1.3 63.3 + - - +
71C LYS* 3.2 26.6 + - - +
72C LYS* 3.8 21.8 - - - +
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Residues in contact with GLN 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C ALA 3.0 12.9 + - - +
66C VAL 3.7 6.5 - - - +
68C ALA* 1.3 72.0 - - - +
70C LEU* 1.3 58.7 + - - +
71C LYS 3.0 5.6 - - - -
72C LYS* 2.9 27.0 + - - +
73C LEU* 3.1 43.7 + - - +
85C PRO* 4.7 1.3 - - - -
302C PRO* 4.0 18.3 - - - +
303C ILE* 4.0 14.4 - - + -
306C VAL* 3.7 25.0 - - + +
1031C EDO 2.7 45.9 + - - -
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Residues in contact with LEU 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C VAL* 2.9 18.4 + - + +
67C GLU* 3.4 9.9 - - - +
68C ALA 3.2 0.4 - - - -
69C GLN* 1.3 76.9 - - - +
71C LYS* 1.3 58.4 + - + +
72C LYS 3.3 0.2 - - - -
73C LEU 4.9 0.2 - - - -
303C ILE* 3.9 25.5 - - + +
58D LEU* 3.4 36.2 - - + +
63D VAL* 4.1 20.0 - - + +
66D VAL* 4.0 19.3 - - + -
67D GLU* 3.5 35.2 - - + +
70D LEU* 4.5 13.5 - - + -
274D PHE* 4.0 13.2 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il